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Cytosine base editors with increased PAM and deaminase motif flexibility for gene editing in zebrafish

Author

Listed:
  • Yu Zhang

    (South China Normal University
    South China Normal University
    Oklahoma Medical Research Foundation)

  • Yang Liu

    (South China Normal University
    South China Normal University)

  • Wei Qin

    (Oklahoma Medical Research Foundation)

  • Shaohui Zheng

    (South China Normal University
    South China Normal University)

  • Jiawang Xiao

    (South China Normal University
    South China Normal University)

  • Xinxin Xia

    (South China Normal University
    South China Normal University)

  • Xuanyao Yuan

    (South China Normal University
    South China Normal University)

  • Jingjing Zeng

    (South China Normal University
    South China Normal University)

  • Yu Shi

    (South China Normal University
    South China Normal University)

  • Yan Zhang

    (South China Normal University
    South China Normal University)

  • Hui Ma

    (Southern Medical University
    Southern Medical University)

  • Gaurav K. Varshney

    (Oklahoma Medical Research Foundation)

  • Ji-Feng Fei

    (Southern Medical University
    Southern Medical University
    South China University of Technology)

  • Yanmei Liu

    (South China Normal University
    South China Normal University)

Abstract

Cytosine base editing is a powerful tool for making precise single nucleotide changes in cells and model organisms like zebrafish, which are valuable for studying human diseases. However, current base editors struggle to edit cytosines in certain DNA contexts, particularly those with GC and CC pairs, limiting their use in modelling disease-related mutations. Here we show the development of zevoCDA1, an optimized cytosine base editor for zebrafish that improves editing efficiency across various DNA contexts and reduces restrictions imposed by the protospacer adjacent motif. We also create zevoCDA1-198, a more precise editor with a narrower editing window of five nucleotides, minimizing off-target effects. Using these advanced tools, we successfully generate zebrafish models of diseases that were previously challenging to create due to sequence limitations. This work enhances the ability to introduce human pathogenic mutations in zebrafish, broadening the scope for genomic research with improved precision and efficiency.

Suggested Citation

  • Yu Zhang & Yang Liu & Wei Qin & Shaohui Zheng & Jiawang Xiao & Xinxin Xia & Xuanyao Yuan & Jingjing Zeng & Yu Shi & Yan Zhang & Hui Ma & Gaurav K. Varshney & Ji-Feng Fei & Yanmei Liu, 2024. "Cytosine base editors with increased PAM and deaminase motif flexibility for gene editing in zebrafish," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53735-y
    DOI: 10.1038/s41467-024-53735-y
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    References listed on IDEAS

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    1. Marion Rosello & Malo Serafini & Luca Mignani & Dario Finazzi & Carine Giovannangeli & Marina C. Mione & Jean-Paul Concordet & Filippo Del Bene, 2022. "Disease modeling by efficient genome editing using a near PAM-less base editor in vivo," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Fang Liang & Yu Zhang & Lin Li & Yexin Yang & Ji-Feng Fei & Yanmei Liu & Wei Qin, 2022. "SpG and SpRY variants expand the CRISPR toolbox for genome editing in zebrafish," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    3. Jeremy Vicencio & Carlos Sánchez-Bolaños & Ismael Moreno-Sánchez & David Brena & Charles E. Vejnar & Dmytro Kukhtar & Miguel Ruiz-López & Mariona Cots-Ponjoan & Alejandro Rubio & Natalia Rodrigo Meler, 2022. "Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    4. Alexis C. Komor & Yongjoo B. Kim & Michael S. Packer & John A. Zuris & David R. Liu, 2016. "Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage," Nature, Nature, vol. 533(7603), pages 420-424, May.
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